1ZYJ

Human P38 MAP Kinase in Complex with Inhibitor 1a

• PDB DOI: https://doi.org/10.2210/pdb1ZYJ/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2005-06-10 Released: 2005-11-08 
• Deposition Author(s): Karpusas, M., Michelotti, E.L., Springman, E.B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.267 
• R-Value Work: 0.243 
• R-Value Observed: 0.260 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 41.94 kDa 
• Atom Count: 2,865 
• Modelled Residue Count: 331 
• Deposited Residue Count: 360 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitogen-activated protein kinase 14	A	360	Homo sapiens	Mutation(s): 0  Gene Names: MAPK14, CSBP, CSBP1, CSBP2, MXI2 EC: 2.7.1.37
UniProt & NIH Common Fund Data Resources
Find proteins for Q16539 (Homo sapiens) Explore Q16539  Go to UniProtKB:  Q16539
PHAROS:  Q16539 GTEx:  ENSG00000112062

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BI5	C [auth A]	4-PHENOXY-N-(PYRIDIN-2-YLMETHYL)BENZAMIDE C19 H16 N2 O2 HVLSCZSVTCNAQX-UHFFFAOYSA-N
BOG	B [auth A]	octyl beta-D-glucopyranoside C14 H28 O6 HEGSGKPQLMEBJL-RKQHYHRCSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
BI5	PDBBind:  1ZYJ	IC50: 1500 (nM) from 1 assay(s)
	BindingDB:  1ZYJ	IC50: 1500 (nM) from 1 assay(s)
	Binding MOAD:  1ZYJ	IC50: 1500 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.267 
• R-Value Work: 0.243 
• R-Value Observed: 0.260 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.76	α = 90
b = 70.92	β = 90
c = 75.8	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-11-08 
Deposition Author(s): Karpusas, M., Michelotti, E.L., Springman, E.B.

Revision History  

• Version 1.0: 2005-11-08
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Data collection, Derived calculations, Structure summary
• Version 1.4: 2023-08-23
  Changes: Data collection, Database references, Refinement description, Structure summary